PDB-2xln: Crystal structure of a complex between Actinomadura R39 DD-peptid...

ID or keywords:

Entry

Database: PDB / ID: 2xln

Title

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

Components

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE,

Keywords

HYDROLASE / PEPTIDOGLYCAN

Function / homology

Function and homology information

serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region
Similarity search - Function

Biological species

ACTINOMADURA SP (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Sauvage, E. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P.

Citation

Journal: Acs Med.Chem.Lett. / Year: 2011
Title: Structure Guided Development of Potent Reversibly Binding Penicillin Binding Protein Inhibitors
Authors: Woon, E.C.Y. / Zervosen, A. / Sauvage, E. / Simmons, K.J. / Ivec, M. / Inglis, S.R. / Fishwick, C.W.G. / Gobec, S. / Charlier, P. / Luxen, A. / Schofield, C.J.

History

Deposition	Jul 21, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 26, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 6, 2012	Group: Database references / Version format compliance
Revision 1.2	Jun 18, 2014	Group: Database references
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2xln.cif.gz	679.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2xln.ent.gz	568.2 KB	Display	PDB format
PDBx/mmJSON format	2xln.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2xln_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	2xln_full_validation.pdf.gz	2 MB	Display
Data in XML	2xln_validation.xml.gz	83.2 KB	Display
Data in CIF	2xln_validation.cif.gz	110.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xl/2xln ftp://data.pdbj.org/pub/pdb/validation_reports/xl/2xln	HTTPS FTP

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Related structure data

Related structure data	2xk1C 1w79 1w8q 1w8y 2vgj 2vgk 2wke 2xdm 2y4a 2y55 2y59 C: citing same article (ref.)
Similar structure data	2xdm-4 2y55-1 2y4a-3 2y59-1 4b4x-1 1w8y-1 2y4a-4 3zvt-4 1w8y-4 3zcz-1 2y59-2 4ben-3 1w8q-2 2y59-4 2y4a-2 2wke-3 2xdm-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#29 - May 2002 Penicillin-binding Proteins similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE,

B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE,

C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE,

D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE,

hetero molecules

203 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE,

hetero molecules

defined by author&software
50.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE,

hetero molecules

defined by author&software
50.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE,

hetero molecules

defined by author&software
50.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE,

hetero molecules

defined by author&software
50.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.994, 91.258, 106.878
Angle α, β, γ (deg.)	90.00, 94.46, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE, / DD-CARBOXYPEPTIDASE / DD-PEPTIDASE / PENICILLIN-BINDING PROTEIN / PBP Mass: 50083.812 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA SP (bacteria) / Strain: R39 References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical	ChemComp-EWA / [(1S)-1-{[(2,6-DIMETHOXYPHENYL)CARBONYL]AMINO}ETHYL]BORONIC ACID Mass: 253.059 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₆BNO₅
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.2 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796
Detector	Type: MARRESEARCH / Date: Jan 25, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 2.4→35.6 Å / Num. obs: 77046 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7 % / R_merge(I) obs: 0.1 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 3.6 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→33.35 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.906 / SU B: 15.878 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24719	3878	5 %	RANDOM
R_work	0.1914	-	-	-
obs	0.19423	73143	99.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 24.847 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.08 Å²	0 Å²	-0.02 Å²
2-	-	0.12 Å²	0 Å²
3-	-	-	-0.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→33.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13394	0	159	816	14369

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.021	13774
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.15	1.974	18846
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.8	5	1858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.472	25.47	574
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.953	15	1920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.22	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	2182
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10676
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.183	0.2	6420
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.296	0.2	9285
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	921
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.243	0.2	126
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.151	0.2	18
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.32	1.5	9341
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.57	2	14556
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.94	3	4944
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.533	4.5	4290
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.301	290	-
R_work	0.23	5365	-
obs	-	-	99.37 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.1095	5.4262	-1.2223	9.8553	-3.4661	5.0802	0.3252	0.1803	-0.1187	-0.2535	-0.3616	0.6178	1.5916	-0.3839	0.0364	0.3305	-0.0755	0.0433	0.3294	0.017	0.3175	-16.403	-21.039	33.256
2	1.0198	-0.1037	-0.0154	0.2593	0.0719	0.8567	-0.0268	-0.0222	0.0392	0.051	0.0422	-0.0467	0.0571	-0.0011	-0.0154	0.0689	0.0153	-0.0325	0.1698	-0.005	0.151	11.705	6.734	41.164
3	1.9163	-0.8599	0.2482	1.1019	0.578	0.6958	-0.0183	-0.0185	-0.1053	-0.0571	-0.1056	0.1123	-0.0104	0.0012	0.1239	0.0611	-0.0109	-0.0345	0.151	0.0065	0.1782	-2.195	20.247	41.404
4	2.4008	0.7663	-0.0882	0.774	0.2766	1.2174	-0.0376	-0.0483	0.0648	0.1067	0.053	-0.1759	-0.0572	0.2158	-0.0153	0.0356	0.0756	-0.0484	0.1508	0.0078	0.134	19.855	8.904	45.238
5	1.6667	0.2839	-0.3481	0.7553	-0.3077	1.6465	-0.0468	0.0338	-0.1984	0.1088	0.048	0.0208	0.2143	-0.084	-0.0012	0.0655	0.0199	-0.0072	0.1035	-0.0043	0.1199	4.701	-10.82	37.747
6	0.9192	1.3158	-1.328	2.213	-1.0554	7.6105	-0.1979	-0.0648	-0.3	0.2569	0.2162	0.0092	0.8729	-0.7007	-0.0182	0.0884	-0.0429	0.0351	0.1894	0.0608	0.1847	-10.125	-18.056	42.059
7	4.8977	1.4326	0.2254	2.897	-0.4299	3.136	-0.2091	0.3328	0.5413	-0.3847	0.0876	0.2513	-0.8268	-0.2409	0.1215	0.2967	0.0876	-0.0676	-0.0768	0.0809	0.0939	54.443	38.659	18.653
8	0.3973	-0.1071	0.1611	1.0137	-0.3364	2.3795	-0.0166	-0.1362	0.0196	0.1809	0.0295	0.0082	-0.062	-0.0788	-0.0128	0.0646	-0.0201	-0.02	0.1247	-0.022	0.1301	59.955	15.502	54.741
9	1.326	-0.2577	-1.4574	0.1715	0.5775	2.3149	-0.0638	-0.2265	-0.0404	0.0445	0.0343	-0.0413	0.183	0.3759	0.0295	0.0521	0.0087	-0.0391	0.1387	0.028	0.1193	76.572	8.692	43.307
10	0.6189	-0.0959	0.2325	1.0573	-0.6629	2.6734	0.0235	-0.1151	0.0589	0.1235	0.0473	0.0639	-0.1314	-0.2289	-0.0709	0.0839	-0.0043	0.0011	0.0805	-0.033	0.1305	55.024	20.069	49.2
11	1.5058	0.3841	-0.5732	1.0362	-1.4428	2.2275	0.0641	-0.1192	0.153	0.1643	-0.0327	-0.0203	-0.5682	0.0899	-0.0314	0.2315	0.0038	0.0046	-0.0324	-0.0081	0.1463	62.25	36.046	34.996
12	4.8264	1.8578	0.3403	6.7936	0.7364	2.935	-0.0258	0.005	0.4823	-0.2869	0.0964	0.0075	-0.6452	0.3214	-0.0706	0.2629	-0.0141	0.0006	-0.0327	0.0397	0.1281	62.004	39.542	24.795
13	8.0174	3.5603	3.6881	6.7396	-1.7298	11.4176	0.7398	-0.687	1.8648	-0.5631	-0.4493	0.0042	-2.0733	-0.6127	-0.2905	0.2808	0.0753	0.0569	0.2904	0.0098	0.2915	13.207	93.735	-30.569
14	0.8822	-0.167	0.1016	1.2885	-0.5631	1.2493	0.0298	-0.1574	-0.0194	0.1663	0.061	0.1347	-0.0338	-0.1425	-0.0908	0.0759	0.0069	0.0328	0.1671	-0.0372	0.1242	13.053	63.129	-3.423
15	2.1679	-0.6165	-1.85	0.3283	0.7204	2.1598	-0.06	-0.2329	-0.1395	0.0517	0.0285	-0.0568	0.0753	0.149	0.0316	0.0985	0.0017	-0.0326	0.055	0.0193	0.128	29.76	51.405	-10.71
16	0.9433	0.0658	-0.0068	0.7497	-0.621	1.308	0.0235	-0.1397	0.0857	0.1977	0.0299	0.125	-0.1201	-0.1764	-0.0534	0.1232	0.0372	0.0281	0.1142	-0.0482	0.1135	10.615	66.247	-2.338
17	0.478	1.1492	-0.0687	3.9983	0.0653	0.4807	-0.0955	0.0628	-0.0072	0.2478	0.0336	-0.2729	-0.2963	-0.0794	0.0619	0.1667	0.0499	-0.0161	0.0714	-0.0237	0.132	25.526	81.057	-14.326
18	2.853	0.3444	0.5457	4.4874	1.8778	3.1828	-0.0051	-0.0128	0.2066	-0.1195	0.085	-0.0592	-0.351	-0.0822	-0.08	0.1056	0.0574	0.01	0.0544	-0.002	0.1337	17.506	83.653	-21.722
19	8.9987	0.1958	-1.181	6.2085	0.9703	4.2641	-0.2237	-0.2443	-0.9059	0.2539	-0.052	-0.9329	0.7887	0.5387	0.2757	0.0142	0.1256	0.1383	-0.0869	0.2995	0.3983	59.662	66.844	25.796
20	1.5337	-0.4627	0.0546	2.3448	-0.7395	1.9369	-0.0711	0.141	0.0134	-0.4579	0.1833	0.3267	-0.0215	-0.5503	-0.1122	0.1522	-0.0867	-0.0297	0.1279	-0.0068	0.1106	25.09	92.229	8.669
21	1.6904	0.8227	-0.2791	1.4	-1.1505	1.076	-0.1442	0.1494	0.0679	-0.2183	-0.0096	-0.172	0.0124	-0.0459	0.1538	0.1418	-0.0237	0.0275	0.0302	-0.0212	0.1533	45.146	103.39	10.278
22	2.9852	-1.3627	0.8766	3.7846	-0.8263	3.1791	-0.1678	0.2573	0.1053	-0.4954	0.1846	0.3599	-0.1172	-0.7324	-0.0168	0.0603	-0.1467	-0.1025	0.2051	0.0401	0.0182	21.278	95.346	5.545
23	1.7558	-0.1563	-0.1438	1.5936	-0.3043	1.4598	-0.1877	-0.0339	-0.3956	-0.3611	0.0137	-0.2477	0.286	-0.0401	0.174	0.1262	-0.0525	0.1177	-0.0289	-0.0186	0.209	44.175	76.248	17.75
24	2.7835	-1.4862	-0.3632	8.3486	3.9947	6.4621	-0.3155	0.0632	-0.7144	-0.7372	0.0434	-0.3043	0.1402	0.8768	0.2722	0.0724	0.0488	0.1689	-0.0678	0.0875	0.4628	61.724	71.613	15.665

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 24
2	X-RAY DIFFRACTION	2	A	25 - 194
3	X-RAY DIFFRACTION	3	A	195 - 249
4	X-RAY DIFFRACTION	4	A	250 - 305
5	X-RAY DIFFRACTION	5	A	306 - 423
6	X-RAY DIFFRACTION	6	A	424 - 466
7	X-RAY DIFFRACTION	7	B	1 - 44
8	X-RAY DIFFRACTION	8	B	45 - 149
9	X-RAY DIFFRACTION	9	B	150 - 250
10	X-RAY DIFFRACTION	10	B	251 - 359
11	X-RAY DIFFRACTION	11	B	360 - 423
12	X-RAY DIFFRACTION	12	B	424 - 465
13	X-RAY DIFFRACTION	13	C	1 - 12
14	X-RAY DIFFRACTION	14	C	13 - 145
15	X-RAY DIFFRACTION	15	C	146 - 247
16	X-RAY DIFFRACTION	16	C	248 - 385
17	X-RAY DIFFRACTION	17	C	386 - 411
18	X-RAY DIFFRACTION	18	C	412 - 465
19	X-RAY DIFFRACTION	19	D	1 - 44
20	X-RAY DIFFRACTION	20	D	45 - 132
21	X-RAY DIFFRACTION	21	D	133 - 251
22	X-RAY DIFFRACTION	22	D	252 - 291
23	X-RAY DIFFRACTION	23	D	292 - 437
24	X-RAY DIFFRACTION	24	D	438 - 466

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